We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies (...) of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

My dissertation explores the nature of artifacts – things like chairs, tables, and pinball machines – and addresses the question of whether there is anything essential to being an artifact and a member of a particular artifact kind. My dissertation offers new arguments against both the anti-essentialist and current essentialist proposals. Roughly put, the view is that artifacts are successful products of an intention to make something with certain features constitutive of an artifact kind. The constitutive features are often functional (...) features, but may include structural, material, aesthetic, and other features. I further explore the ways in which artifacts are mind-dependent and I argue that this dependence is disjunctive. Not only do they depend on the intentions of their makers, but they also can depend on social groups or public norms and thus artifacts have an importantly social dimension and I argue that this disjunctive account applies not to artifact kinds but to individual artifacts depending on their context of creation. (shrink)

Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lower-level processes and higher-level systems capacities are degenerate. The diachronic underdetermination problem regards the problem of reverse engineering a system where the non-linear relations between system capacities and lower-level mechanisms are (...) changing over time. Braun and Marom argue that recent insights to biological complexity leave the aim of reverse engineering hopeless - in principle as well as in practice. While I support their call for systemic approaches to capture the dynamic nature of living systems, I take issue with the conflation of reverse engineering with naïve reductionism. I clarify how the notion of design principles can be more broadly conceived and argue that reverse engineering is compatible with a dynamic view of organisms. It may even help to facilitate an integrated account that bridges the gap between mechanistic and systems approaches. (shrink)

According to conventional wisdom, local gauge symmetry is not a symmetry of nature, but an artifact of how our theories represent nature. But a study of the so-called theta-vacuum appears to refute this view. The ground state of a quantized non-Abelian Yang-Mills gauge theory is characterized by a real-valued, dimensionless parameter theta—a fundamental new constant of nature. The structure of this vacuum state is often said to arise from a degeneracy of the vacuum of the corresponding classical theory, which degeneracy (...) allegedly arises from the fact that “large” (but not “small”) local gauge transformations connect physically distinct states of zero field energy. If that is right, then some local gauge transformations do generate empirical symmetries. In defending conventional wisdom against this challenge I hope to clarify the meaning of empirical symmetry while deepening our understanding of gauge transformations. I distinguish empirical from theoretical symmetries. Using Galileo’s ship and Faraday’s cube as illustrations, I say when an empirical symmetry is implied by a theoretical symmetry. I explain how the theta-vacuum arises, and how “large” gauge transformations differ from “small” ones. I then present two analogies from elementary quantum mechanics. By applying my analysis of the relation between empirical and theoretical symmetries, I show which analogy faithfully portrays the character of the vacuum state of a classical non-Abelian Yang-Mills gauge theory. The upshot is that “large” as well as “small” gauge transformations are purely formal symmetries of non-Abelian Yang-Mills gauge theories, whether classical or quantized. It is still worth distinguishing between these kinds of symmetries. An analysis of gauge within the constrained-Hamiltonian formalism yields the result that “large” gauge transformations should not be classified as gauge transformations; indeed, nor should “global” gauge transformations. In a theory in which boundary conditions are modeled dynamically, “global” gauge transformations may be associated with physical symmetries, corresponding to translations of these extra dynamical variables. Such translations are symmetries if and only if charge is conserved. But it is hard to argue that these symmetries are empirical, and in any case they do not correspond to any constant phase change in a quantum state. (shrink)

This volume collects papers presented at the Founding Conference of the European Philosophy of Science Association meeting, held November 2007. It provides an excellent overview of the state of the art in philosophy of science in different European countries.

Canguilhem criticized the concept of “public health”: health and disease are concepts that only apply to individuals, taken as organic totalities. Their extension to a different level of organization is purely metaphorical. The importance assumed by epidemiology in the construction of our knowledge of the normal and the pathological does, however, call for reflection on the role and the status of the population level of organization in our approach to health phenomena. The entanglement of the biological and the social in (...) human life and in contemporary societies justifies this level of analysis for better understanding the complexity and the interaction of health determinants both at the level of individuals and their interactions and at that of the population. But is this population level just a useful level of analysis that makes it possible to bring to light the social determinants of health at the individual level, or does it rest instead on characteristics of the population that are irreducible to individual characteristics, but which are nevertheless important for understanding and taking action with respect to both population and individual health? Defending this second alternative, I show how the epidemiological point of view, and in particular that of social epidemiology, leads us to rethink the possibility of a concept of “population health” that is not reducible to the sum of individual instances of health. (shrink)